## [1] "O76_p4_con_R1_2.hicup.bam"

Truncation & Mapping

Truncation Frequency

Category Read 1 Read 2
Total 83,976,768 83,976,768
Not Truncated 49,754,625 47,242,494
Truncated 34,222,143 36,734,274

Truncated Read Length

Category Read 1 Read 2
Average Length Truncated 47.6 47.9

Mapping Efficiency

Category Read 1 Read 2
Too Short To Map 4,735,654 4,722,713
Unique Alignments 72,611,776 70,587,608
Multiple Alignments 2,684,238 2,819,963
Failed To Align 3,945,100 5,846,484
Paired 61,860,138 61,860,138

Truncation and Mapping Bar Plot

Filtering

Filtering Breakdown by Category

Category Count
Valid Pairs 34,589,649
Invalid Pairs 27,270,489
Same Circularised 103,129
Same Dangling Ends 2,747,237
Same Fragment Internal 11,321,757
Re Ligation 8,896,972
Contiguous Sequence 416,123
Wrong Size 3,785,271
Total Pairs 61,860,138

Filtering Breakdown Pie Chart

Ditag Length Distribution

Frequency Line Plot

Deduplication

Deduplication Summary Table

Category All Ditags Unique Ditags
Read Pairs 34,589,649 45,717
Cis-close (<10Kbp) 5,924,917 5,559
Cis-far (>10Kbp) 21,296,797 24,789
Trans 7,367,935 15,369

Deduplication Bar Chart

Analysis produced by HiCUP - a tool for mapping and performing quality control on Hi-C data

Babraham Bioinformatics